The stray grain was observed in electron beam welded (EBW) joint of single crystal molybdenum (Mo). Finite element (FE) method, combining the theoretical analysis, is used for evaluating the stray grain formation. Temperature-dependent thermal properties of molybdenum are incorporated in the model and a 3D volumetric moving double-ellipsoid heat source is applied. The relationship between parameter Φ, describing the degree of stray grain formation, and the thermal gradient G and the growth velocity V is used. Temperature and thermal gradient data of the model are extracted from simulation results under different operating conditions, and Φ is calculated. The effects of the welding parameters, including welding power Q and welding speed S on the formation of the weld stray grain are obtained.